Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell transcriptomics and chromatin accessibility in human fetal microglia

ABSTRACT: Single cell transcriptomics and chromatin accessibility in human fetal microglia

PROVIDER: PRJNA594973 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10669900_1.fastq.gz	Fastqsanger.gz
	SRR10669900_2.fastq.gz	Fastqsanger.gz
	SRR10670000_1.fastq.gz	Fastqsanger.gz
	SRR10670000_2.fastq.gz	Fastqsanger.gz
	SRR10669901_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 494

Similar Datasets

Single cell transcriptomics and chromatin accessibility in human fetal microglia

Project description:Microglia, the myeloid cells of the central nervous system (CNS), are heterogeneous and exhibit distinct stages during mouse development; however, human microglia development is not elucidated. Here, single cell gene expression profiles of 15,782 human microglia and bulk chromatin profiles were assessed in 23 fetuses during development from gestational week (GW) 9 to 18. Microglia are highly heterogeneous at all developmental stages and exhibit transcriptional profiles similar to a phagocytic microglia phenotype associated with disease. Microglia start to mature during this developmental period and increasingly express homeostatic and sensome markers at later gestational stages. Concomitantly, chromatin accessibility increases in microglia from older fetuses with underlying transcriptional networks reminiscent of adult microglia. In conclusion, this work demonstrates that microglia already progress to a more mature, immune-sensing competent phenotype during early human fetal development, which might render microglia vulnerable towards environmental or inflammatory perturbations during early pregnancy.

2020-07-31 | GSE141862 | GEO

A human cell atlas of fetal chromatin accessibility

Project description:A human cell atlas of fetal chromatin accessibility

| PRJNA629599 | ENA

scATAC-seq of fetal thymus

Project description:To investigate the gene regulatory mechanisms driving T cell development, we generated single-cell transcriptomics and chromatin accessibility data from a human fetal thymus sample at 10 weeks of gestation.

2021-11-30 | E-MTAB-9828 | biostudies-arrayexpress

scRNA-seq of human fetal thymus

2021-11-30 | E-MTAB-9840 | biostudies-arrayexpress

Chromatin Accessibility in Developing Human Brain

Project description:<p>Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. To obtain a high resolution depiction of chromatin structure and gene expression in developing human fetal cortex, we dissected the post-conception week (PCW) 15-17 human neocortex into two major anatomical divisions to distinguish between proliferating neural progenitors and post mitotic neurons: (1) GZ: the neural progenitor-enriched region encompassing the ventricular zone (VZ), subventricular zone (SVZ), and intermediate zone (IZ) and (2) CP: the neuron-enriched region containing the subplate (SP), cortical plate (CP), and marginal zone (MZ). Tissues were obtained from three independent donors and three to four technical replicates from each tissue were processed for ATAC-seq to define the landscape of accessible chromatin and RNA-seq for genome-wide gene expression profiling.</p>

| phs001438 | dbGaP

Microglia and Fn14 regulate transcription and chromatin accessibility in developing neurons

Project description:Microglia and Fn14 regulate transcription and chromatin accessibility in developing neurons

| PRJNA774832 | ENA

A human cell atlas of fetal chromatin accessibility

Project description:We devised an improved assay for single cell profiling of chromatin accessibility with three-level combinatorial indexing (sci-ATAC-seq3). We applied this method to 53 fetal tissue samples representing 15 organs, altogether profiling approximately one million single cells. We leveraged cell types defined by gene expression in the same organs to annotate these data, and built a catalog of hundreds-of-thousands of candidate gene regulatory elements exhibiting cell type-specific accessibility. Our analyses focus on the properties of lineage-specific transcription factors, organ-specific specializations of broadly distributed cell types, and cell type-specific enrichments of complex trait heritability. Additional data formats are available at atlas.brotmanbaty.org.

2020-11-01 | GSE149683 | GEO

Epigenetic profiling of microglia-specific gene transcription and chromatin accessibility in mouse forebrain after chronic mild stress

Project description:Multiple studies have suggested that stress induces neuroinflammation and contributes to emotion-related behavioral deficits. To study epigenetic changes in microglia after chronic stress, we purified microglia from mouse brain after exposure to chronic unexpected mild stress (CUMS), and then performed RNA-seq and ATAC-seq to study microglia-specific alterations of transcriptome and chromatin accessibility in response to chronic stress.

2022-12-31 | GSE186760 | GEO

Genome-wide open chromatin status in WT and IRF8KO microglia

Project description:The role of a transcription factor, Interferon Regulatory Factor 8 (IRF8), in microglia is yet to be fully understood. We conducted a study to examine the chromatin status of postnatal and adult wild-type (WT) and IRF8-knockout (IRF8KO) microglia through ATAC-Seq. We also added 5xFAD Alzheimer's disease microglia to observe any chromatin events that may be similar in disease-associated microglia. After deep-sequencing and differential analysis, we discovered that chromatin accessibility in microglia is dependent on IRF8. In the absence of IRF8, there was aberrant chromatin accessibility that potentially resulted in mRNA transcription of genes that were upregulated in IRF8KO microglia, which was distinct from 5xFAD microglia. This study contributes to a better understanding of epigenetic regulation in microglia.

2024-07-01 | GSE266421 | GEO

Acute BAF perturbation causes immediate changes in chromatin accessibility

Project description:Loss-of-function mutations in genes coding for subunits of the large, multifarious BRG1/BRM associated factor (BAF) chromatin remodeling complexes are frequently causative for cancer or developmental diseases1-5. Cells lacking the most frequently mutated subunits like the ATPase SMARCA4 typically exhibit drastic chromatin accessibility changes, especially of important regulatory regions6-12. However, so far it remains unknown how these changes are established over time, and whether they are causative for intra-complex synthetic lethalities abrogating the formation (SMARCC1-SMARCC2)8,13,14 or activity (SMARCA4-SMARCA2)15-17 of BAF complexes. Here, we utilize the dTAG system18 to induce acute degradation of BAF subunits in wild-type and BAF mutant backgrounds and analyze the resulting chromatin accessibility changes with high kinetic resolution. We observe that chromatin alterations are established faster than the duration of one cell cycle and that maintaining genome accessibility requires constant ATP-dependent remodeling. Completely abolishing BAF complex function by acute degradation of a synthetic lethal subunit in a paralog-deficient background results in a near-complete loss of chromatin accessibility at BAF-controlled sites, especially at super-enhancers, providing a mechanism for intra-complex synthetic lethalities.

2020-12-23 | PXD018381 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data